Regulatory Sequence Analysis Tools

Welcome to Regulatory Sequence Analysis Tools (RSAT).

This web site provides a series of modular computer programs specifically designed for the detection of regulatory signals in non-coding sequences.

RSAT servers have been up and running since 1997. The project was initiated by Jacques van Helden, and is now pursued by the RSAT team.

This website is free and open to all users.

Which program to use ? A guide to our main tools for new users. 1 - Choose your type of data to analyse Choose Data type ChIP-seq List of gene names Sequences Matrices (PSSM) Coordinates (BED) List of variants 2 - Choose your biological question / analysis to perform Choose selection Which TF motifs are over-represented in this data set ? I want to extract their promoter sequences (or other sequence features) Which regulatory elements are conserved in promoters of orthologs ? (only for prokaryotes and fungi) Are there over-represented motifs in these sequences ? I want to scan these sequences with a motif I want to scan sequences with these matrices I want to compare matrices (with known collections) I want to cluster and align matrices I want to convert the matrix format I want to extract the sequences corresponding to these coordinates Obtain the variants and their flanking sequences Which transcription factor binding sites are affected by these variants ? 3 - Relevant RSAT programs Choose selection peak-motifs retrieve sequences retrieve Ensembl sequences (only for organisms supported at Ensembl.org) footprint discovery footprint-scan oligo-analysis (words) dyad-analysis (spaced pairs) dna-pattern matrix-scan (quick) matrix-scan (full options) matrix-scan (quick) matrix-scan (full options) compare matrices matrix clustering convert matrix fetch sequences from UCSC (only for organisms supported at genome.ucsc.edu) retrieve variation sequences scan variations Complete list of online tools is in the left menu

Check latest RSAT paper in NAR web software issue 2015 Check RSAT tutorial at ECCB'14 and all training material Learn how to use Peak-motifs with a Nature Protocol [view article] Try our new programs

hosted by Institut FranÇais de Bioinformatique (IFB), Paris, France	hosted by Centro de Ciencias Genomicas (CCG), Cuernavaca, Mexico	hosted by Institut FranÇais de Bioinformatique (IFB), Paris, France
hosted by Institut FranÇais de Bioinformatique (IFB), Paris, France	hosted by Lab Computational & structural biology, EEAD-CSIC, Zaraagoza, Spain	hosted by Institut FranÇais de Bioinformatique (IFB), Paris, France

92 organisms supported on roscoff2 (http://rsat.sb-roscoff.fr/) . Group specificity: Metazoa

Citing RSAT complete suite of tools:

• New ! Medina-Rivera A, Defrance M, Sand O, Herrmann C, Castro-Mondragon J, Delerce J, Jaeger S, Blanchet C, Vincens P, Caron C, Staines DM, Contreras-Moreira B, Artufel M, Charbonnier-Khamvongsa L, Hernandez C, Thieffry D, Thomas-Chollier M, van Helden J (2015) RSAT 2015: Regulatory Sequence Analysis Tools . Nucleic Acids Res. 2015 (Web Server issue) in press. [Full text]
• Thomas-Chollier M, Defrance M, Medina-Rivera A, Sand O, Herrmann C, Thieffry D, van Helden J. (2011) RSAT 2011: regulatory sequence analysis tools. Nucleic Acids Res. 2011 Jul;39(Web Server issue):W86-91. [Pubmed 21715389] [Full text]
• Thomas-Chollier, M., Sand, O., Turatsinze, J. V., Janky, R., Defrance, M., Vervisch, E., Brohee, S. & van Helden, J. (2008). RSAT: regulatory sequence analysis tools. Nucleic Acids Res. [Pubmed 18495751] [Full text]
• van Helden, J. (2003). Regulatory sequence analysis tools. Nucleic Acids Res. 2003 Jul 1;31(13):3593-6. [Pubmed 12824373] [Full text] [pdf]

For citing individual tools: the reference of each tool is indicated on top of their query form.
All RSAT publications and all publications for the Network Analysis Tools.

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RSAT logos designed by Mauricio Guzman (http://www.altamirastudio.com.mx/)

For suggestions or information request, please contact :
Jacques van Helden (Jacques.van-Helden@univ-amu.fr)

Running with RSAT code from : Feb 16 17:12:44 2023

Software error:

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For help, please send mail to the webmaster (rootmaster@sb-roscoff.fr), giving this error message and the time and date of the error.